NLGN3neuroligin 3

Score

Autism Reports / Total Reports

Rare Variants / Common Variants

27 / 5

Aliases

NLGN3, HNL3, ASPGX1, AUTSX1, KIAA1480

Associated Syndromes

-

Genetic Category

Rare Single Gene Mutation

Chromosome Band

Xq13.1

Associated Disorders

-

Relevance to Autism

Studies have found rare single gene variations in the NLGN3 gene in autism. However, other studies claimed to find no rare variations in the NLGN3 gene in autism patients, although one of these found several silent variations. One study (Ylisaukko-oja et al., 2005) found a genetic association between an NLGN3 variant and autism in a sample of Finnish autism families, and another study (Yu et al., 2011) found a genetic association between an NLGN3 variant and autism in the Chinese Han population. This gene was identified by TADA (transmission and de novo association) analysis of a combined dataset from the Simons Simplex Collection (SSC) and the Autism Sequencing Consortium (ASC) as a gene strongly enriched for variants likely to affect ASD risk with a false discovery rate (FDR) of <0.1 (Sanders et al., 2015); among the variants identified in this gene was one de novo loss-of-function (L

Molecular Function

This gene encodes a member of a family of neuronal cell-adhesion proteins located at the postsynaptic side of the synapse. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses.

SFARI Gene score

2

Strong Candidate

A series of rare, deleterious variants have been reported in autism (Jamain et al., 2003 and Sanders et al., 2011; PMID: 21658581), and a gene expression study of lymphoblasts suggests reduced expression of the gene in ASD (Yasuda et al., 2011; PMID: 21615902). NLGN3 interacts with another ASD gene, NRXN1. This gene was recently identified by TADA (transmission and de novo association) analysis of a combined dataset from the Simons Simplex Collection (SSC) and the Autism Sequencing Consortium (ASC) as a gene strongly enriched for variants likely to affect ASD risk with a false discovery rate (FDR) of <0.1 (Sanders et al., 2015).

criteria met

Strong Candidate

We considered a rigorous statistical comparison between cases and controls, yielding genome-wide statistical significance, with independent replication, to be the strongest possible evidence for a gene. These criteria were relaxed slightly for category 2.

04-01-2017

2

Initial score established: 2

Description

A series of rare, deleterious variants have been reported in autism (Jamain et al., 2003 and Sanders et al., 2011; PMID: 21658581), and a gene expression study of lymphoblasts suggests reduced expression of the gene in ASD (Yasuda et al., 2011; PMID: 21615902). NLGN3 interacts with another ASD gene, NRXN1. This gene was recently identified by TADA (transmission and de novo association) analysis of a combined dataset from the Simons Simplex Collection (SSC) and the Autism Sequencing Consortium (ASC) as a gene strongly enriched for variants likely to affect ASD risk with a false discovery rate (FDR) of <0.1 (Sanders et al., 2015).